diff options
| author | Armin Pirkovitsch <sperber@FreeBSD.org> | 2012-12-01 00:00:43 +0000 |
|---|---|---|
| committer | Armin Pirkovitsch <sperber@FreeBSD.org> | 2012-12-01 00:00:43 +0000 |
| commit | 2b222ce70ca5b2e52bbae33a07a577f32c9a12b5 (patch) | |
| tree | 0762d28ea40b794fecacaa8fa8d19b9afa9689f3 /biology/tinker | |
| parent | 9c5386b239ade6b8468ddd1c77a4454d54be727c (diff) | |
| download | ports-2b222ce70ca5b2e52bbae33a07a577f32c9a12b5.tar.gz ports-2b222ce70ca5b2e52bbae33a07a577f32c9a12b5.zip | |
Notes
Diffstat (limited to 'biology/tinker')
| -rw-r--r-- | biology/tinker/Makefile | 80 | ||||
| -rw-r--r-- | biology/tinker/distinfo | 4 | ||||
| -rw-r--r-- | biology/tinker/files/patch-aa | 207 | ||||
| -rw-r--r-- | biology/tinker/files/patch-ah | 5 | ||||
| -rw-r--r-- | biology/tinker/files/patch-ai | 5 | ||||
| -rw-r--r-- | biology/tinker/files/patch-aj | 5 | ||||
| -rw-r--r-- | biology/tinker/files/patch-bench__bench1.run | 5 | ||||
| -rw-r--r-- | biology/tinker/files/patch-bench__bench2.run | 5 | ||||
| -rw-r--r-- | biology/tinker/files/patch-bench__bench3.run | 5 | ||||
| -rw-r--r-- | biology/tinker/files/patch-bench__bench4.run (renamed from biology/tinker/files/patch-ak) | 4 | ||||
| -rw-r--r-- | biology/tinker/files/patch-bench__bench5.run (renamed from biology/tinker/files/patch-al) | 4 | ||||
| -rw-r--r-- | biology/tinker/files/patch-make__Makefile | 211 | ||||
| -rw-r--r-- | biology/tinker/files/patch-source_openend.f (renamed from biology/tinker/files/patch-openend.f) | 4 | ||||
| -rw-r--r-- | biology/tinker/files/pkg-message.in | 6 | ||||
| -rw-r--r-- | biology/tinker/pkg-plist | 991 |
15 files changed, 788 insertions, 753 deletions
diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile index 7035071bbaf1..3e3fb3a2899e 100644 --- a/biology/tinker/Makefile +++ b/biology/tinker/Makefile @@ -1,76 +1,74 @@ -# New ports collection makefile for: tinker -# Date Created: 26 August 1998 -# Whom: Glenn Johnson -# +# Created by: Glenn Johnson # $FreeBSD$ -# PORTNAME= tinker -PORTVERSION= 5.1.09 +PORTVERSION= 6.1.01 CATEGORIES= biology MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/ MAINTAINER= ports@FreeBSD.org COMMENT= A general purpose molecular modelling package -MAKE_ENV+= HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}" +RESTRICTED= author requests no distribution except from his FTP site + +OPTIONS_DEFINE= OPTIMIZED_FFLAGS DATA DOCS EXAMPLES +OPTIONS_DEFAULT=DATA +OPTIMIZED_FFLAGS_DESC= compilation optimizations -WRKSRC= ${WRKDIR}/tinker/source +WRKSRC= ${WRKDIR}/${PORTNAME} +BUILD_WRKSRC= ${WRKSRC}/source +INSTALL_WRKSRC= ${WRKSRC}/source -MAKEFILE= ${WRKDIR}/tinker/make/Makefile +USE_FORTRAN= yes +MAKE_ENV= HAVE_G2C=yes +MAKEFILE= ${WRKSRC}/make/Makefile ALL_TARGET= all listing INSTALL_TARGET= rename -RESTRICTED= author requests no distribution except from his FTP site +MAKE_JOBS_SAFE= yes -DOCS= 0README *.pdf *.txt announce/release* -SAMPLES= 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.run *.xyz +SUB_FILES= pkg-message + +DOCS= 0README *.pdf *.txt +SAMPLES= 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz BENCHES= 0README *.dyn0 *.log *.key *.run *.xyz results* .include <bsd.port.pre.mk> -USE_FORTRAN= yes - -.if defined(WITH_OPTIMIZED_FLAGS) +.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations .if (${ARCH} == "i386") FFLAGS+= -mfancy-math-387 -malign-double .endif # i386 .endif -pre-everything:: -.if !defined(WITH_OPTIMIZED_FLAGS) - @${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes." +.if empty(PORT_OPTIONS:MDATA) +NOPORTDATA= yes .endif post-extract: - ${CHMOD} -R u+w ${WRKDIR}/tinker - -post-patch: - @${REINPLACE_CMD} -e 's|%%FFLAGS%%|${FFLAGS}|g' ${WRKSRC}/../make/Makefile + @${CHMOD} -R u+w ${WRKSRC} post-install: + @${MKDIR} ${DATADIR} + ${INSTALL_DATA} ${INSTALL_WRKSRC}/tinker.txt ${DATADIR} @${MKDIR} ${DATADIR}/params - @${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \ - ${DATADIR} - @${INSTALL_DATA} ${WRKDIR}/tinker/params/* \ - ${DATADIR}/params -.if !defined(NOPORTDOCS) - @${MKDIR} ${DOCSDIR} - @${MKDIR} ${EXAMPLESDIR} + ${INSTALL_DATA} ${WRKSRC}/params/* ${DATADIR}/params +.if ${PORT_OPTIONS:MDATA} @${MKDIR} ${DATADIR}/bench + ${INSTALL_DATA} ${BENCHES:S|^|${WRKSRC}/bench/|} ${DATADIR}/bench @${MKDIR} ${DATADIR}/test - @${INSTALL_DATA} ${DOCS:S|^|${WRKDIR}/tinker/doc/|} ${DOCSDIR} - @${INSTALL_DATA} ${SAMPLES:S|^|${WRKDIR}/tinker/example/|} ${EXAMPLESDIR} - @${INSTALL_DATA} ${BENCHES:S|^|${WRKDIR}/tinker/bench/|} ${DATADIR}/bench - @${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${DATADIR}/test + ${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test +.endif +.if ${PORT_OPTIONS:MDOCS} + @${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${DOCS:S|^|${WRKSRC}/doc/|} ${DOCSDIR} +.endif +.if ${PORT_OPTIONS:MEXAMPLES} + @${MKDIR} ${EXAMPLESDIR} + ${INSTALL_DATA} ${SAMPLES:S|^|${WRKSRC}/example/|} ${EXAMPLESDIR} .endif - @${ECHO_MSG} "" - @${ECHO_MSG} " **********************************************************" - @${ECHO_MSG} " The author requests that you return a license form " - @${ECHO_MSG} " to him if you find Tinker to be useful. " - @${ECHO_MSG} " " - @${ECHO_MSG} " See ${DOCSDIR} for license forms. " - @${ECHO_MSG} " **********************************************************" - @${ECHO_MSG} "" + @${ECHO_CMD} + @${CAT} ${PKGMESSAGE} + @${ECHO_CMD} .include <bsd.port.post.mk> diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo index d441f5ba5b8a..2971eb293037 100644 --- a/biology/tinker/distinfo +++ b/biology/tinker/distinfo @@ -1,2 +1,2 @@ -SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183 -SIZE (tinker-5.1.09.tar.gz) = 14071638 +SHA256 (tinker-6.1.01.tar.gz) = fa287c381fd866822b19396fa152406b8463421f0a27902867cdbbf6b67233e4 +SIZE (tinker-6.1.01.tar.gz) = 19478639 diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa deleted file mode 100644 index e68ae52123d0..000000000000 --- a/biology/tinker/files/patch-aa +++ /dev/null @@ -1,207 +0,0 @@ ---- ../make/Makefile.orig 2010-08-25 00:58:16.000000000 +0400 -+++ ../make/Makefile 2011-01-22 01:12:41.000000000 +0300 -@@ -9,8 +9,8 @@ - ## - ## 1. make all Build all the TINKER executables - ## 2. make rename Move the executables to BINDIR --## 3. make remove_links Create soft links in LINKDIR --## 4. make create_links Remove soft links from LINKDIR -+## 3. make remove_links Remove soft links in LINKDIR -+## 4. make create_links Create soft links from LINKDIR - ## 6. make listing Concatenate source to tinker.txt - ## 5. make clean Delete objects and executables - ## -@@ -30,9 +30,9 @@ - ## LINKDIR Linked Copies of TINKER Executables - ## - --TINKERDIR = /Users/ponder/tinker --BINDIR = $(TINKERDIR)/bin --LINKDIR = /usr/local/bin -+TINKERDIR = ${WRKDIR} -+BINDIR = ${PREFIX}/bin -+#LINKDIR = /usr/local/bin - - #################################################################### - ## Known Machine Types; Uncomment One of the Following Sections ## -@@ -40,6 +40,20 @@ - #################################################################### - - ## -+## Machine: IntelPC / FreeBSD -+## CPU Type: Intel, AMD, Cyrix -+## Oper Sys: FreeBSD 4.2 -+## Compiler: f77 , aka g77 -+## -+ -+F77 = ${FC} -+LIBS = -+F77FLAGS = -c %%FFLAGS%% -+LINKFLAGS = -+OPTFLAGS = -+LIBFLAGS = -rcuv -+ -+## - ## Machine: Generic Linux - ## CPU Type: Intel x86 Compatible - ## Oper Sys: Fedora Core -@@ -102,12 +116,12 @@ - ## Compiler: Intel Fortran for Mac 11 - ## - --F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort --LIBS = --F77FLAGS = -c -axSSSE3 -vec-report0 --OPTFLAGS = -O3 -no-ipo -no-prec-div --LIBFLAGS = -crusv --LINKFLAGS = -static-intel -mmacosx-version-min=10.4 -+#F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort -+#LIBS = -+#F77FLAGS = -c -axSSSE3 -vec-report0 -+#OPTFLAGS = -O3 -no-ipo -no-prec-div -+#LIBFLAGS = -crusv -+#LINKFLAGS = -static-intel -mmacosx-version-min=10.4 - - ## - ## Machine: Macintosh (PPC) -@@ -584,6 +598,8 @@ - xyzpdb.x \ - xyzsybyl.x - -+.SUFFIXES: .x -+ - .f.o: - ${F77} ${F77FLAGS} ${OPTFLAGS} $*.f - -@@ -596,8 +612,8 @@ - server.o: - ${F77} ${F77FLAGS} ${OPTFLAGS} server.f - --%.x: %.o libtinker.a -- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS} -+.o.x: libtinker.a -+ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} - - all: ${EXEFILES} - -@@ -608,63 +624,63 @@ - cat *.i *.f > tinker.txt - - rename: -- mv alchemy.x $(BINDIR)/alchemy -- mv analyze.x $(BINDIR)/analyze -- mv anneal.x $(BINDIR)/anneal -- mv archive.x $(BINDIR)/archive -- mv correlate.x $(BINDIR)/correlate -- mv crystal.x $(BINDIR)/crystal -- mv diffuse.x $(BINDIR)/diffuse -- mv distgeom.x $(BINDIR)/distgeom -- mv document.x $(BINDIR)/document -- mv dynamic.x $(BINDIR)/dynamic -- mv gda.x $(BINDIR)/gda -- mv intedit.x $(BINDIR)/intedit -- mv intxyz.x $(BINDIR)/intxyz -- mv minimize.x $(BINDIR)/minimize -- mv minirot.x $(BINDIR)/minirot -- mv minrigid.x $(BINDIR)/minrigid -- mv monte.x $(BINDIR)/monte -- mv newton.x $(BINDIR)/newton -- mv newtrot.x $(BINDIR)/newtrot -- mv nucleic.x $(BINDIR)/nucleic -- mv optimize.x $(BINDIR)/optimize -- mv optirot.x $(BINDIR)/optirot -- mv optrigid.x $(BINDIR)/optrigid -- mv path.x $(BINDIR)/path -- mv pdbxyz.x $(BINDIR)/pdbxyz -- mv polarize.x $(BINDIR)/polarize -- mv poledit.x $(BINDIR)/poledit -- mv potential.x $(BINDIR)/potential -- mv prmedit.x $(BINDIR)/prmedit -- mv protein.x $(BINDIR)/protein -- mv pss.x $(BINDIR)/pss -- mv pssrigid.x $(BINDIR)/pssrigid -- mv pssrot.x $(BINDIR)/pssrot -- mv radial.x $(BINDIR)/radial -- mv saddle.x $(BINDIR)/saddle -- mv scan.x $(BINDIR)/scan -- mv sniffer.x $(BINDIR)/sniffer -- mv spacefill.x $(BINDIR)/spacefill -- mv spectrum.x $(BINDIR)/spectrum -- mv superpose.x $(BINDIR)/superpose -- mv sybylxyz.x $(BINDIR)/sybylxyz -- mv testgrad.x $(BINDIR)/testgrad -- mv testhess.x $(BINDIR)/testhess -- mv testpair.x $(BINDIR)/testpair -- mv testrot.x $(BINDIR)/testrot -- mv timer.x $(BINDIR)/timer -- mv timerot.x $(BINDIR)/timerot -- mv valence.x $(BINDIR)/valence -- mv vibbig.x $(BINDIR)/vibbig -- mv vibrate.x $(BINDIR)/vibrate -- mv vibrot.x $(BINDIR)/vibrot -- mv xtalfit.x $(BINDIR)/xtalfit -- mv xtalmin.x $(BINDIR)/xtalmin -- mv xyzedit.x $(BINDIR)/xyzedit -- mv xyzint.x $(BINDIR)/xyzint -- mv xyzpdb.x $(BINDIR)/xyzpdb -- mv xyzsybyl.x $(BINDIR)/xyzsybyl -+ ${INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy -+ ${INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze -+ ${INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal -+ ${INSTALL_PROGRAM} archive.x $(BINDIR)/archive -+ ${INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate -+ ${INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal -+ ${INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse -+ ${INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom -+ ${INSTALL_PROGRAM} document.x $(BINDIR)/document -+ ${INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic -+ ${INSTALL_PROGRAM} gda.x $(BINDIR)/gda -+ ${INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit -+ ${INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz -+ ${INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize -+ ${INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot -+ ${INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid -+ ${INSTALL_PROGRAM} monte.x $(BINDIR)/monte -+ ${INSTALL_PROGRAM} newton.x $(BINDIR)/newton -+ ${INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot -+ ${INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic -+ ${INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize -+ ${INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot -+ ${INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid -+ ${INSTALL_PROGRAM} path.x $(BINDIR)/path -+ ${INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz -+ ${INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize -+ ${INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit -+ ${INSTALL_PROGRAM} potential.x $(BINDIR)/potential -+ ${INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit -+ ${INSTALL_PROGRAM} protein.x $(BINDIR)/protein -+ ${INSTALL_PROGRAM} pss.x $(BINDIR)/pss -+ ${INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid -+ ${INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot -+ ${INSTALL_PROGRAM} radial.x $(BINDIR)/radial -+ ${INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle -+ ${INSTALL_PROGRAM} scan.x $(BINDIR)/scan -+ ${INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer -+ ${INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill -+ ${INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum -+ ${INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose -+ ${INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz -+ ${INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad -+ ${INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess -+ ${INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair -+ ${INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot -+ ${INSTALL_PROGRAM} timer.x $(BINDIR)/timer -+ ${INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot -+ ${INSTALL_PROGRAM} valence.x $(BINDIR)/valence -+ ${INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig -+ ${INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate -+ ${INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot -+ ${INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit -+ ${INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin -+ ${INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit -+ ${INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint -+ ${INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb -+ ${INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl - - remove_links: - rm -f $(LINKDIR)/alchemy diff --git a/biology/tinker/files/patch-ah b/biology/tinker/files/patch-ah deleted file mode 100644 index 12bd7c9ac00d..000000000000 --- a/biology/tinker/files/patch-ah +++ /dev/null @@ -1,5 +0,0 @@ ---- ../bench/bench1.run.orig Tue Jul 24 14:02:20 2001 -+++ ../bench/bench1.run Wed Sep 5 13:57:02 2001 -@@ -1 +1 @@ --../bin/timer bench1 1 y -+timer bench1 1 y diff --git a/biology/tinker/files/patch-ai b/biology/tinker/files/patch-ai deleted file mode 100644 index e5a6559bb29f..000000000000 --- a/biology/tinker/files/patch-ai +++ /dev/null @@ -1,5 +0,0 @@ ---- ../bench/bench2.run.orig Tue Jul 24 14:02:20 2001 -+++ ../bench/bench2.run Wed Sep 5 13:58:47 2001 -@@ -1 +1 @@ --../bin/timer bench2 1 y -+timer bench2 1 y diff --git a/biology/tinker/files/patch-aj b/biology/tinker/files/patch-aj deleted file mode 100644 index 3e18d09b5071..000000000000 --- a/biology/tinker/files/patch-aj +++ /dev/null @@ -1,5 +0,0 @@ ---- ../bench/bench3.run.orig Wed Sep 5 14:00:09 2001 -+++ ../bench/bench3.run Wed Sep 5 14:01:27 2001 -@@ -1 +1 @@ --time ../bin/vibrate bench3 0 -+time vibrate bench3 0 diff --git a/biology/tinker/files/patch-bench__bench1.run b/biology/tinker/files/patch-bench__bench1.run new file mode 100644 index 000000000000..7b728a8884f7 --- /dev/null +++ b/biology/tinker/files/patch-bench__bench1.run @@ -0,0 +1,5 @@ +--- bench/bench1.run.orig Tue Jul 24 14:02:20 2001 ++++ bench/bench1.run Wed Sep 5 13:57:02 2001 +@@ -1 +1 @@ +-../bin/timer bench1 1 y ++timer bench1 1 y diff --git a/biology/tinker/files/patch-bench__bench2.run b/biology/tinker/files/patch-bench__bench2.run new file mode 100644 index 000000000000..b9f70cc453d8 --- /dev/null +++ b/biology/tinker/files/patch-bench__bench2.run @@ -0,0 +1,5 @@ +--- bench/bench2.run.orig Tue Jul 24 14:02:20 2001 ++++ bench/bench2.run Wed Sep 5 13:58:47 2001 +@@ -1 +1 @@ +-../bin/timer bench2 1 y ++timer bench2 1 y diff --git a/biology/tinker/files/patch-bench__bench3.run b/biology/tinker/files/patch-bench__bench3.run new file mode 100644 index 000000000000..fc1db99f32dd --- /dev/null +++ b/biology/tinker/files/patch-bench__bench3.run @@ -0,0 +1,5 @@ +--- bench/bench3.run.orig Wed Sep 5 14:00:09 2001 ++++ bench/bench3.run Wed Sep 5 14:01:27 2001 +@@ -1 +1 @@ +-time ../bin/vibrate bench3 0 ++time vibrate bench3 0 diff --git a/biology/tinker/files/patch-ak b/biology/tinker/files/patch-bench__bench4.run index 9a415fcd0f32..177ddfb84e36 100644 --- a/biology/tinker/files/patch-ak +++ b/biology/tinker/files/patch-bench__bench4.run @@ -1,5 +1,5 @@ ---- ../bench/bench4.run.orig Tue Jul 24 14:02:20 2001 -+++ ../bench/bench4.run Wed Sep 5 14:02:17 2001 +--- bench/bench4.run.orig Tue Jul 24 14:02:20 2001 ++++ bench/bench4.run Wed Sep 5 14:02:17 2001 @@ -1,3 +1,3 @@ cp bench4.dyn0 bench4.dyn -time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0 diff --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-bench__bench5.run index 4fa7ddb6faf4..c047178b3ec7 100644 --- a/biology/tinker/files/patch-al +++ b/biology/tinker/files/patch-bench__bench5.run @@ -1,5 +1,5 @@ ---- ../bench/bench5.run.orig 2010-08-25 00:58:15.000000000 +0400 -+++ ../bench/bench5.run 2011-01-26 23:35:18.000000000 +0300 +--- bench/bench5.run.orig 2010-08-25 00:58:15.000000000 +0400 ++++ bench/bench5.run 2011-01-26 23:35:18.000000000 +0300 @@ -1,3 +1,3 @@ cp bench5.dyn0 bench5.dyn -time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0 diff --git a/biology/tinker/files/patch-make__Makefile b/biology/tinker/files/patch-make__Makefile new file mode 100644 index 000000000000..47ea46a155cb --- /dev/null +++ b/biology/tinker/files/patch-make__Makefile @@ -0,0 +1,211 @@ +--- make/Makefile.orig 2012-06-29 14:51:42.000000000 +0900 ++++ make/Makefile 2012-11-10 00:12:19.000000000 +0900 +@@ -9,8 +9,8 @@ + ## + ## 1. make all Build all the TINKER executables + ## 2. make rename Move the executables to BINDIR +-## 3. make remove_links Create soft links in LINKDIR +-## 4. make create_links Remove soft links from LINKDIR ++## 3. make remove_links Remove soft links in LINKDIR ++## 4. make create_links Create soft links from LINKDIR + ## 6. make listing Concatenate source to tinker.txt + ## 5. make clean Delete objects and executables + ## +@@ -30,9 +30,9 @@ + ## LINKDIR Linked Copies of TINKER Executables + ## + +-TINKERDIR = /Users/ponder/tinker +-BINDIR = $(TINKERDIR)/bin +-LINKDIR = /usr/local/bin ++TINKERDIR = ${WRKDIR} ++BINDIR = ${PREFIX}/bin ++#LINKDIR = /usr/local/bin + + #################################################################### + ## Known Machine Types; Uncomment One of the Following Sections ## +@@ -40,6 +40,20 @@ + #################################################################### + + ## ++## Machine: IntelPC / FreeBSD ++## CPU Type: Intel, AMD, Cyrix ++## Oper Sys: FreeBSD 4.2 ++## Compiler: f77 , aka g77 ++## ++ ++F77 = ${FC} ++LIBS = ++F77FLAGS = -c ${FFLAGS} ++LINKFLAGS = ${LDFLAGS} ++OPTFLAGS = ++LIBFLAGS = -rcuv ++ ++## + ## Machine: Generic Linux + ## CPU Type: Intel x86 Compatible + ## Oper Sys: Fedora Core +@@ -104,12 +118,12 @@ + ## Parallel: OpenMP + ## + +-F77 = /opt/intel/bin/ifort +-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 +-F77FLAGS = -c -axSSSE3 -assume cc_omp +-OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp +-LIBFLAGS = -crusv +-LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 ++#F77 = /opt/intel/bin/ifort ++#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 ++#F77FLAGS = -c -axSSSE3 -assume cc_omp ++#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp ++#LIBFLAGS = -crusv ++#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 + + ## + ## Machine: Macintosh +@@ -592,6 +606,8 @@ + xyzpdb.x \ + xyzsybyl.x + ++.SUFFIXES: .x ++ + .f.o: + ${F77} ${F77FLAGS} ${OPTFLAGS} $*.f + +@@ -601,8 +617,8 @@ + server.o: + ${F77} ${F77FLAGS} ${OPTFLAGS} server.f + +-%.x: %.o libtinker.a +- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ ++.o.x: libtinker.a ++ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} + + all: ${EXEFILES} + +@@ -613,65 +629,65 @@ + cat *.i *.f *.c > tinker.txt + + rename: +- mv alchemy.x $(BINDIR)/alchemy +- mv analyze.x $(BINDIR)/analyze +- mv anneal.x $(BINDIR)/anneal +- mv archive.x $(BINDIR)/archive +- mv correlate.x $(BINDIR)/correlate +- mv crystal.x $(BINDIR)/crystal +- mv diffuse.x $(BINDIR)/diffuse +- mv distgeom.x $(BINDIR)/distgeom +- mv document.x $(BINDIR)/document +- mv dynamic.x $(BINDIR)/dynamic +- mv gda.x $(BINDIR)/gda +- mv intedit.x $(BINDIR)/intedit +- mv intxyz.x $(BINDIR)/intxyz +- mv minimize.x $(BINDIR)/minimize +- mv minirot.x $(BINDIR)/minirot +- mv minrigid.x $(BINDIR)/minrigid +- mv molxyz.x $(BINDIR)/molxyz +- mv monte.x $(BINDIR)/monte +- mv newton.x $(BINDIR)/newton +- mv newtrot.x $(BINDIR)/newtrot +- mv nucleic.x $(BINDIR)/nucleic +- mv optimize.x $(BINDIR)/optimize +- mv optirot.x $(BINDIR)/optirot +- mv optrigid.x $(BINDIR)/optrigid +- mv path.x $(BINDIR)/path +- mv pdbxyz.x $(BINDIR)/pdbxyz +- mv polarize.x $(BINDIR)/polarize +- mv poledit.x $(BINDIR)/poledit +- mv potential.x $(BINDIR)/potential +- mv prmedit.x $(BINDIR)/prmedit +- mv protein.x $(BINDIR)/protein +- mv pss.x $(BINDIR)/pss +- mv pssrigid.x $(BINDIR)/pssrigid +- mv pssrot.x $(BINDIR)/pssrot +- mv radial.x $(BINDIR)/radial +- mv saddle.x $(BINDIR)/saddle +- mv scan.x $(BINDIR)/scan +- mv sniffer.x $(BINDIR)/sniffer +- mv spacefill.x $(BINDIR)/spacefill +- mv spectrum.x $(BINDIR)/spectrum +- mv superpose.x $(BINDIR)/superpose +- mv sybylxyz.x $(BINDIR)/sybylxyz +- mv testgrad.x $(BINDIR)/testgrad +- mv testhess.x $(BINDIR)/testhess +- mv testpair.x $(BINDIR)/testpair +- mv testrot.x $(BINDIR)/testrot +- mv timer.x $(BINDIR)/timer +- mv timerot.x $(BINDIR)/timerot +- mv torsfit.x $(BINDIR)/torsfit +- mv valence.x $(BINDIR)/valence +- mv vibbig.x $(BINDIR)/vibbig +- mv vibrate.x $(BINDIR)/vibrate +- mv vibrot.x $(BINDIR)/vibrot +- mv xtalfit.x $(BINDIR)/xtalfit +- mv xtalmin.x $(BINDIR)/xtalmin +- mv xyzedit.x $(BINDIR)/xyzedit +- mv xyzint.x $(BINDIR)/xyzint +- mv xyzpdb.x $(BINDIR)/xyzpdb +- mv xyzsybyl.x $(BINDIR)/xyzsybyl ++ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy ++ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze ++ ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal ++ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive ++ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate ++ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal ++ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse ++ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom ++ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document ++ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic ++ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda ++ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit ++ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz ++ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize ++ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot ++ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid ++ ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz ++ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte ++ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton ++ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot ++ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic ++ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize ++ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot ++ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid ++ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path ++ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz ++ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize ++ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit ++ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential ++ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit ++ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein ++ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss ++ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid ++ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot ++ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial ++ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle ++ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan ++ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer ++ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill ++ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum ++ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose ++ ${BSD_INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz ++ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad ++ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess ++ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair ++ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot ++ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer ++ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot ++ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit ++ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence ++ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig ++ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate ++ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot ++ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit ++ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin ++ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit ++ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint ++ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb ++ ${BSD_INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl + + remove_links: + rm -f $(LINKDIR)/alchemy diff --git a/biology/tinker/files/patch-openend.f b/biology/tinker/files/patch-source_openend.f index ad2afdc47adf..5745f93d0a8a 100644 --- a/biology/tinker/files/patch-openend.f +++ b/biology/tinker/files/patch-source_openend.f @@ -1,8 +1,8 @@ $FreeBSD$ ---- openend.f.orig Fri Apr 18 13:31:51 2003 -+++ openend.f Mon Jul 21 13:36:11 2003 +--- source/openend.f.orig Fri Apr 18 13:31:51 2003 ++++ source/openend.f Mon Jul 21 13:36:11 2003 @@ -29,11 +29,11 @@ c c standard Fortran 90, unavailable in some Fortran 77 compilers diff --git a/biology/tinker/files/pkg-message.in b/biology/tinker/files/pkg-message.in new file mode 100644 index 000000000000..97777e8a5a27 --- /dev/null +++ b/biology/tinker/files/pkg-message.in @@ -0,0 +1,6 @@ +********************************************************** + The author requests that you return a license form + to him if you find Tinker to be useful. + + See %%DOCSDIR%% for license forms. +**********************************************************" diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist index a83b64406249..9b6dc9d419a3 100644 --- a/biology/tinker/pkg-plist +++ b/biology/tinker/pkg-plist @@ -14,6 +14,7 @@ bin/intxyz bin/minimize bin/minirot bin/minrigid +bin/molxyz bin/monte bin/newton bin/newtrot @@ -45,6 +46,7 @@ bin/testpair bin/testrot bin/timer bin/timerot +bin/torsfit bin/valence bin/vibbig bin/vibrate @@ -58,424 +60,429 @@ bin/xyzsybyl %%PORTDOCS%%%%DOCSDIR%%/0README %%PORTDOCS%%%%DOCSDIR%%/ffe-guide.pdf %%PORTDOCS%%%%DOCSDIR%%/guide.pdf -%%PORTDOCS%%%%DOCSDIR%%/guide.txt %%PORTDOCS%%%%DOCSDIR%%/license.pdf %%PORTDOCS%%%%DOCSDIR%%/license.txt -%%PORTDOCS%%%%DOCSDIR%%/release-3.2 -%%PORTDOCS%%%%DOCSDIR%%/release-3.6 -%%PORTDOCS%%%%DOCSDIR%%/release-3.7 -%%PORTDOCS%%%%DOCSDIR%%/release-3.8 -%%PORTDOCS%%%%DOCSDIR%%/release-3.9 -%%PORTDOCS%%%%DOCSDIR%%/release-4.0 -%%PORTDOCS%%%%DOCSDIR%%/release-4.1 -%%PORTDOCS%%%%DOCSDIR%%/release-4.2 %%PORTDOCS%%%%DOCSDIR%%/summary.pdf %%PORTDOCS%%%%DOCSDIR%%/summary.txt -%%PORTDOCS%%%%EXAMPLESDIR%%/0README -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.int -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.key -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.seq -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.key -%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.key -%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.key -%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/arach.int -%%PORTDOCS%%%%EXAMPLESDIR%%/arach.key -%%PORTDOCS%%%%EXAMPLESDIR%%/arach.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.int -%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.key 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